My brain seems to work differently than everyone else, so my system is a little unique. I do it in a file cabinet like system. That has 3 major categories than each of those into sub categories. The 3 major are single, double, and multiple.
Single: vellum(transparent, lace, etc.), cardstock, texture, pattern, and fancy
Double: vellum, texture, sets (like the ones that are left & right different but go together), cardstock, pattern, and fancy
Multiple: vellum, cardstock, texture, pattern, and fancy
As for once into the separate files then they go into ROYGBIV(or rainbow) color scheme. Those are just my loose paper organization. I hope this helps and you find a good way to organize.